High resolution imaging of tissue proteins

Abstract

The present invention provides labeling method for Array Tomography (AT) and immunohistochemistry (IHC) that enables automated analysis many tens-to-hundreds of proteins in a manner that minimizes tissue degradation, increases data fidelity, and substantially increases throughput and reduces cost. Also included are methods for automated acquisition of AT and IHC data.

What is claimed is: 
     
         1 . A method comprising:
 contacting an intact tissue sample with at least one binding ligand that binds a particular protein, wherein said at least one binding ligand is linked to a nucleic acid label; and   detecting said nucleic acid label, thereby detecting the presence of said particular protein in said intact tissue sample.   
     
     
         2 . The method of  claim 1 , comprising contacting said intact tissue sample with a plurality of binding ligands, wherein each binding ligand that binds a particular protein is linked to a unique nucleic acid label. 
     
     
         3 - 5 . (canceled) 
     
     
         6 . The method of  claim 1 , wherein the method comprises embedding said intact tissue sample in a resin such that said intact tissue sample is sliced into sections of thickness between 20 and 1000 nm. 
     
     
         7 . The method of  claim 1 , wherein said nucleic acid label comprises a nucleic acid oligomer. 
     
     
         8 . (canceled) 
     
     
         9 . The method of  claim 1 , further comprising contacting said intact tissue sample to a detection label that comprises a nucleic acid oligomer, wherein said detection label comprises a sequence which is complementary to a sequence of said nucleic acid label. 
     
     
         10 . The method of  claim 9 , wherein said detection label comprises at least one detection tag. 
     
     
         11 - 12 . (canceled) 
     
     
         13 . The method of  claim 1 , wherein said binding ligand is linked to said nucleic acid label by a non-cleavable linker. 
     
     
         14 - 20 . (canceled) 
     
     
         21 . The method of  claim 1 , wherein detecting comprises determining a sequence of each said nucleic acid label by sequencing by synthesis or sequencing by hybridization. 
     
     
         22 - 27 . (canceled) 
     
     
         28 . The method of  claim 1 , wherein contacting said intact tissue sample with said ligand comprises application of an electric field. 
     
     
         29 - 31 . (canceled) 
     
     
         32 . A system for identifying the protein composition of an intact tissue comprising:
 an intact tissue sample;   at least one binding ligand that binds a particular protein in said intact tissue sample, wherein said binding ligand is linked to a unique nucleic acid label; and   a detector for detection of said nucleic acid label.   
     
     
         33 . The system of  claim 32 , wherein said intact tissue sample is resin embedded and has a section of thickness between 20 and 1000 nm. 
     
     
         34 . The system of  claim 32 , wherein said nucleic acid label comprises a nucleic acid oligomer. 
     
     
         35 . The system of  claim 32 , comprising a plurality of binding ligands, wherein each said binding ligand that binds a specific protein is linked to a unique nucleic acid label. 
     
     
         36 . (canceled) 
     
     
         37 . The system of  claim 32 , further comprising a detection label that comprises a nucleic acid oligomer, wherein said detection label comprises a sequence which is complementary to a sequence of said nucleic acid label. 
     
     
         38 . The system of  claim 37 , wherein said detection label comprises at least one detection tag. 
     
     
         39 . The system of  claim 32 , wherein said binding ligand is linked to said nucleic acid label by a non-cleavable linker. 
     
     
         40 . The system of  claim 32 , wherein said detection comprises determining the a sequence of each nucleic acid label by sequencing by synthesis or sequencing by hybridization. 
     
     
         41 - 42 . (canceled) 
     
     
         43 . The system of any of  claim 32 , further comprising an electric field generator for the application of an electric field during contact of said at least one binding ligand with said intact tissue sample. 
     
     
         44 - 45 . (canceled) 
     
     
         46 . The system of  claim 32 , wherein said at least one binding ligand is selected from ankyrin repeat proteins, anticalins, cysteine knottin scaffolds, cyclic peptides, fynomers, affitins, sso7d, fibronectins, affibodies, and Gp2 protein or fragments thereof. 
     
     
         47 . A kit, said kit comprising:
 at least one binding ligand that binds a particular protein in an intact tissue sample, wherein said binding ligand is linked to a unique nucleic acid label;   a first set of reagents for use when contacting the at least one binding ligand with said tissue sample; and   a second set of reagents for use in detection of said nucleic acid label.   
     
     
         48 - 49 . (canceled)